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- PDB-2a2v: The solution structure of Jingzhaotoxin-XI -

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Basic information

Entry
Database: PDB / ID: 2a2v
TitleThe solution structure of Jingzhaotoxin-XI
ComponentsJingzhaotoxin-XI
KeywordsTOXIN / ICK motif / neurotoxin spider
Function / homologyHuwentoxin-1 family / Ion channel inhibitory toxin / ion channel inhibitor activity / sodium channel regulator activity / potassium channel regulator activity / toxin activity / extracellular region / Kappa-theraphotoxin-Cg1a 1
Function and homology information
Biological speciesChilobrachys jingzhao (spider)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsLiao, Z. / Liang, S.P.
CitationJournal: To be published
Title: The solution structure of Jingzhaotoxin-XI
Authors: Liao, Z. / Liang, S.P.
History
DepositionJun 23, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Jingzhaotoxin-XI


Theoretical massNumber of molelcules
Total (without water)3,7381
Polymers3,7381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Jingzhaotoxin-XI


Mass: 3738.343 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chilobrachys jingzhao (spider) / Secretion: venom / References: UniProt: P0C247
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 5mM Jingzhaotoxin-XI 1H, 20mM phosphate buffer NA, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20 / pH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR softwareName: X-PLOR / Version: NIH2.9.6 / Classification: refinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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